> There is a related (and for PE very serious for rare PDB files) bug in > Chime regarding alignment of group (residue) names. It would be best if > Jmol can handle residue names in any alignment of the three-character > field, e.g. A__, _A_, __A, PC_, _PC.
The current Jmol implementation would *not* handle this.
OK, good that I asked.
However, I do not believe that it will be difficult to change, and I don't forsee any negative impact.
Agreed.
Q: Is it the case that it needs to deal with unaligned group names within the same file? As in, three atoms in the same residue identified with three different column alignments ... A__, _A_, __A
One would hope that within one PDB file the author (or software generating it) would be consistent, but one keeps finding surprises even in published files supposedly compatible with the PDB format specification. So if it is not too hard to parse these terms in a totally robust manner, better to do so.
That would mean I think that "select a" ideally should find all three of the alignments you list above. At the moment I can't think of any reason why different alignments could legitimately be used to distinguish different things.
> The bug in Chime is that while it > can "select pc", it fails to report the selected group name with "show > residue".
I don't understand what "show residue" is supposed to do. Please advise.
There are a series of "show" commands
show atom[s] show residue[s] [bug in Chime: plural doesn't work] show chain[s]
What these do is list via MessageCallback the designated entities that are *currently selected*.
I use these to enable PE's javascript to discern what has been selected, often to generate complex scripts, sometimes with recursive select, report, select, report cycles. Cation-pi and salt-briges are such examples within PE.
I vaguely recall maybe Tim Driscoll requested or implemented this: A command would be extremely useful that expands the currently selected atom set to all groups/residues including selected atoms, or all chains including selected atoms. However, it is still useful for PE/javascript to be able to find out the selected lists, for reporting purposes, but probably in many cases also for dynamic scripting.
> This causes PE to be unable to do cation-pi displays with e.g. > 2MCP as documented at > http://molvis.sdsc.edu/protexpl/cationpi.htm#t3 > (I seem to recall this may have to do with alignment, but I'm not sure > -- may be confusing this bug with another one.)
I looked at this briefly, but wasn't able to understand it.
Forget this. It was just an example that I documented, hence could find and "remember".
-Eric
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